Variant report

Variant	rs12375677
Chromosome Location	chr9:8714991-8714992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10977256	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs10977258	0.84[EUR][1000 genomes]
rs1368979	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1434260	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1821429	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865340	0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs1877447	0.85[CEU][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1991931	0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2053126	0.81[EUR][1000 genomes]
rs6477327	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7866681	0.86[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7866922	0.85[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs906635	0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs906636	0.80[JPT][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs980404	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv892235	chr9:8700396-8865925	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv6474	chr9:8706602-8751414	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1025800	chr9:8712487-9030627	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv539980	chr9:8712487-9030627	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8699600-8717800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:8700800-8718000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:8704400-8731800	Weak transcription	Fetal Lung	lung
4	chr9:8706800-8718000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:8710600-8733600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:8712000-8715800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:8712000-8716600	Weak transcription	Brain Angular Gyrus	brain
8	chr9:8712000-8718200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:8712200-8717800	Weak transcription	Brain Hippocampus Middle	brain
10	chr9:8714600-8715000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:8714800-8717400	Weak transcription	Brain Substantia Nigra	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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